Merge branch 'master' of github.com:fiji/TrackMate

tinevez · tinevez · commit fa490e17730a · 2022-01-15T10:56:33.000+01:00
diff --git a/src/main/java/fiji/plugin/trackmate/TrackMate.java b/src/main/java/fiji/plugin/trackmate/TrackMate.java
@@ -414,7 +414,11 @@ private boolean processGlobal( final SpotGlobalDetectorFactory factory, final Im
 				for ( int frame = settings.tstart; frame <= settings.tend; frame++ )
 				{
 					final List< Spot > spotsThisFrame = new ArrayList<>();
-					for ( final Spot spot : rawSpots.iterable( frame, false ) )
+					final Iterable< Spot > spotsIt = rawSpots.iterable( frame, false );
+					if ( spotsIt == null )
+						continue;
+
+					for ( final Spot spot : spotsIt )
 					{
 						if ( settings.roi.contains(
 								( int ) Math.round( spot.getFeature( Spot.POSITION_X ) / calibration[ 0 ] ),
diff --git a/src/main/java/fiji/plugin/trackmate/util/FileChooser.java b/src/main/java/fiji/plugin/trackmate/util/FileChooser.java
@@ -28,6 +28,7 @@
 import java.io.File;
 import java.io.FilenameFilter;
 import java.util.Locale;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import javax.swing.JFileChooser;
 import javax.swing.filechooser.FileFilter;
@@ -176,19 +177,33 @@ else if ( parent != null && parent instanceof Dialog )
 			/*
 			 * Try with a FilenameFilter (may silently fail).
 			 */
+			final AtomicBoolean workedWithFilenameFilter = new AtomicBoolean( false );
 			if ( fileFilter != null )
 			{
 				final FilenameFilter filenameFilter = new FilenameFilter()
 				{
+					private boolean firstTime = true;
+
 					@Override
 					public boolean accept( final File dir, final String name )
 					{
+						if ( firstTime )
+						{
+							workedWithFilenameFilter.set( true );
+							firstTime = false;
+						}
+
 						return fileFilter.accept( new File( dir, name ) );
 					}
 				};
 				fd.setFilenameFilter( filenameFilter );
 				fd.setVisible( true );
 			}
+			if ( fileFilter == null || ( isMac() && !workedWithFilenameFilter.get() ) )
+			{
+				fd.setFilenameFilter( null );
+				fd.setVisible( true );
+			}
 
 			final String filename = fd.getFile();
 			if ( filename != null )
diff --git a/src/main/java/fiji/plugin/trackmate/util/JLabelLogger.java b/src/main/java/fiji/plugin/trackmate/util/JLabelLogger.java
@@ -64,7 +64,16 @@ public LoggerInJLabel( final JLabel label )
 		@Override
 		public void log( final String message, final Color color )
 		{
-			label.setText( message );
+			
+			final String msg;
+			if (null == message)
+				msg = "null"; // Help debug.
+			else if ( message.startsWith( "<html>" ) )
+				msg = message;
+			else
+				msg = "<html>" + message + "</html>";
+
+			label.setText( msg );
 			label.setForeground( color );
 		}
 

Original file line number	Diff line number	Diff line change
`@@ -414,7 +414,11 @@ private boolean processGlobal( final SpotGlobalDetectorFactory factory, final Im`
`414`	`414`	`for ( int frame = settings.tstart; frame <= settings.tend; frame++ )`
`415`	`415`	`{`
`416`	`416`	`final List< Spot > spotsThisFrame = new ArrayList<>();`
`417`		`- for ( final Spot spot : rawSpots.iterable( frame, false ) )`
	`417`	`+ final Iterable< Spot > spotsIt = rawSpots.iterable( frame, false );`
	`418`	`+ if ( spotsIt == null )`
	`419`	`+ continue;`
	`420`	`+`
	`421`	`+ for ( final Spot spot : spotsIt )`
`418`	`422`	`{`
`419`	`423`	`if ( settings.roi.contains(`
`420`	`424`	`( int ) Math.round( spot.getFeature( Spot.POSITION_X ) / calibration[ 0 ] ),`